[gt-users] Tallymer to get k-mers in a specific range?

[Dan Bolser]

Hi All, Stefan,

I've just read through the Tallymer manual, so apologies if this
question is obvious...

I have a large set of reads, and I'd like to extract all k-mers (the
sequences) with occurrence between 200 and 250 (mitochondrially
derived).

I can't seem to see a way to do that with the Tallymer tools...


Also, I'd like to plot the k-mer frequency distribution for a given
k-mer length, i.e. given a k-mer length of 51, how many k-mers occur 1
time, 2 times, 3 times, ... x times. etc. I can't see how to do this
directly.


The best I can come up with is creating a fake sequence file with all
possible k-mers in it and passing that to search, but I'm sure this
information should be available directly from one of the index files.


Thanks for any help with these issues.

All the best,
Dan.